User: C4

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C40
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Posts by C4

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Comment: C: Removing contaminating reads from human genome
... Thanks GenoMax, would you suggest using the adaptor-trimmed reads (in my case nextera adaptors) or the raw reads (with adaptors) for bbsplit? Also, is it a good idea to use ambiguous=all and ambiguous2=all ? , since ambiguous are the reads with multiple top-scoring mapping locations. ...
written 7 weeks ago by C40
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Comment: C: Removing contaminating reads from human genome
... Hi Genomax, only a few samples have that issue. I determined it using kraken. There is same amout of contamination in all of them (~30%) However in my experience, removing bacterial reads may give better downstream results. I have used bbsplit in the past, as you suggested, but it gave me even less ...
written 7 weeks ago by C40
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Removing contaminating reads from human genome
... Hi, below is my "bbduk" command to remove bacterial reads from human DNA reads. The problem is that mapping percentage to the human genome is decreasing as it also removes bacterial reads. Is there a way around to make it more stringent without reducing mapping % to human genome, currently I think ...
alignment next-gen sequencing written 7 weeks ago by C40 • updated 7 weeks ago by _r_am32k
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Comment: C: Antibiotics in lysis/wash buffers
... Thanks ATpoint, I would actually really like to discuss 1) how to reduce bacterial contamination? 2)I have many reads that simply do not map to human genome, and upon using Kraken, they seem to match pseudomonas specifically, so I am not sure what you mean by BLAST artifacts? ...
written 7 weeks ago by C40
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Comment: C: Removing fastq duplicates
... My understanding was that dedupe would work better if I bbmerge R1+R2. However, wouldn't clumped_headers have all the R1 and R2 fastq headers that got clumped and deduped. So, I could just use those clumped_headers to filter out R1 and R2, instead of only merged+clumped headers. ...
written 7 weeks ago by C40
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Comment: C: Antibiotics in lysis/wash buffers
... Hi, this is a common problem in NGS, which leads to bacterial reads come through in a NGS library. Hence, I wanted to see if someone had opinions on that. ...
written 7 weeks ago by C40
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Comment: C: Removing fastq duplicates
... Hi GenoMax, thanks a lot for this. Your work-around works really well, however I am losing many reads, because of which my mapping% is decreasing. I believe that is just because I do not have very good data. Could you tell me why you suggested finding common between merged and clumped? Why couldn't ...
written 7 weeks ago by C40
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(Closed) Antibiotics in lysis/wash buffers
... H, In my recent ATAC-seq experiments, I am seeing some bacterial contamination, specifically pseudomonas, these are frozen postmortem human brains, so all dead cells. I am wondering if it would be a good idea to add antibioitcs in the wash buffer? If someone has experience with that, please let me k ...
next-gen written 7 weeks ago by C40
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Comment: C: Removing fastq duplicates
... Would you suggest using bbmerge prior to using clumpify dedup for paired-end fastq files. I take this from here, where they suggest using bbmerge and concatenating merged and unmerged fastq files before clumpify, since when paired-end reads are provided, clumpify clumps only based on R1 https://jgi. ...
written 8 weeks ago by C40
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Comment: C: Removing fastq duplicates
... Hi geomax, thanks a lot! I am using k=90 as my reads are 100bps, so as to remove more exact duplicates. This is my fastqc duplication before clumpify: https://ibb.co/yRtkNY8 This is after clumpify: https://ibb.co/Bck0Gtm I will also post the stats that I get after using cumpify with default ...
written 8 weeks ago by C40

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